Cell clustering, visualization, and cell-type annotation Principal component analysis (PCA) was performed with 20 principal components (PCs, determined by Elbow plot), followed by Uniform Manifold Approximation and Projection (UMAP) using the same number of PCs. Next, the cells were clustered using...
An outstanding goal in modern genomics is to systematically predict the functional outcome of noncoding variation associated with complex traits. To address this, we developed Hi-C-coupled multi-marker analysis of genomic annotation (H-MAGMA), which builds on traditional MAGMA—a gene-based analysis...
Several annotation tools such as SNPnexus and VariED are publicly available; however, none of them can use transcript IDs as input and provide the corresponding genomic positions of variants. Results In this study, we developed an R package, called transcript annotation tool (TransAT), that ...
Results of this analysis indicate that genetic variation in different components of the immunosuppression pathway may be susceptibility loci of breast cancer among women of European ancestry. The main strengths of the present analysis were its large sample size, the uniform genotyping procedures and ...
GO annotation enrichment analyses were conducted based on a Benjamini and Hochberg false discovery rate correction with significance set at p < 0.05 by using the Cytoscape plug-in BiNGO[26]. We mapped the sequence reads and contigs using SOAP http://soap.genomics.org.cn/soapaligner.html; ...
--annotate_variation=./annotate_variation.pl The Annovar perl script of annotate_variation.pl -d humandb, --database_locat=humandb The database location/dir for the Annovar annotation datasets EXAMPLE ./InterVar.py -c config.ini # Run the examples in config.ini ./InterVar.py -b hg19 -i...
597 markers (98.98%) were commonly assigned to the same chromosomes, while 583 markers (1.02%) were mapped to different chromosomes in the two genome assemblies. Gene annotation of 56,597 SNP markers was retrieved from IWGSC RefSeq v2.1, 50,006 markers were located in the genic region, 901...
GO annotation [30] was used to determine if the modules had unique functional properties and/or were associated with distinct subcellular compartments (see e.g., [13]). For example, the pink module was enriched for GO biological processes that included the following: central nervous system devel...
Several central metabolic pathways were reconstructed forR. toruloidesBOT-A2 based on the functional annotation and the RNAseq results (Fig.3). In general, in the reconstructed metabolic network (Fig.3), around a third of the genes were significantly differentially expressed while also having a |...
Intel Software: Computer Vision Annotation Tool: A Universal Approach to Data Annotation VentureBeat: Intel open-sources CVAT, a toolkit for data labeling Online Demo Onepanel has added CVAT as an environment into their platform and a running demo of CVAT can be accessed at CVAT Public Demo. If...